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- PDB-8xa0: penton capsomer of the VZV C-capsid -

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Basic information

Entry
Database: PDB / ID: 8xa0
Titlepenton capsomer of the VZV C-capsid
Components
  • (Capsid vertex component ...) x 2
  • Large tegument protein deneddylase
  • Major capsid protein
  • Tri1
  • Tri2A
  • Tri2B
KeywordsVIRUS / VZV / capsid structure
Function / homology
Function and homology information


nuclear capsid assembly / viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / chromosome organization / viral penetration into host nucleus ...nuclear capsid assembly / viral genome packaging / deNEDDylase activity / T=16 icosahedral viral capsid / viral tegument / symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / deubiquitinase activity / viral DNA genome replication / chromosome organization / viral penetration into host nucleus / viral capsid / host cell / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis
Similarity search - Function
Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 / Herpesvirus UL25 family ...Herpesvirus large tegument protein deneddylase / Herpesvirus UL36 tegument protein / Large tegument protein deneddylase / Herpesvirus capsid vertex component 1 / Herpesvirus UL17 protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile. / Herpesvirus large tegument protein, USP domain / Herpesvirus tegument protein, N-terminal conserved region / Herpesvirus UL25 / Herpesvirus UL25 family / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Capsid vertex component 1 / Capsid vertex component 2 / Large tegument protein deneddylase / Major capsid protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsNan, W. / Lei, C. / Xiangxi, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Hlife / Year: 2024
Title: Insights into varicella-zoster virus assembly from the B- and C-capsid at near-atomic resolution structures
Authors: Cao, L. / Wang, N. / Lv, Z. / Chen, W. / Chen, Z. / Song, L. / Sha, X. / Wang, G. / Hu, Y. / Lian, X. / Cui, G. / Fan, J. / Quan, Y. / Liu, H. / Hou, H. / Wang, X.
History
DepositionDec 1, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: Large tegument protein deneddylase
A: Major capsid protein
C: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
h: Capsid vertex component 1
q: Capsid vertex component 2
u: Capsid vertex component 2
y: Large tegument protein deneddylase
R: Tri2A
V: Tri2B
Z: Tri1


Theoretical massNumber of molelcules
Total (without water)957,32713
Polymers957,32713
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 1 types, 2 molecules 2y

#1: Protein/peptide Large tegument protein deneddylase


Mass: 5500.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: UL36 / Production host: Homo sapiens (human)
References: UniProt: P10220, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Protein , 4 types, 8 molecules ACEFGRVZ

#2: Protein
Major capsid protein / MCP


Mass: 152365.312 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: ORF40, MCP, ORF 40, HHV3_E_SVETAgp42, HHV3_gp42, HHV3gp42
Production host: Homo sapiens (human) / References: UniProt: Q6QCL5
#5: Protein Tri2A


Mass: 27729.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
#6: Protein Tri2B


Mass: 28721.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)
#7: Protein Tri1


Mass: 32268.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human)

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Capsid vertex component ... , 2 types, 3 molecules hqu

#3: Protein Capsid vertex component 1


Mass: 73998.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: CVC1, UL17 / Production host: Homo sapiens (human) / References: UniProt: P10201
#4: Protein Capsid vertex component 2


Mass: 10890.343 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: CVC2, UL25 / Production host: Homo sapiens (human) / References: UniProt: P10209

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human alphaherpesvirus 3 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human alphaherpesvirus 3 (Varicella-zoster virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 417864 / Symmetry type: POINT

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